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fix docs: rST-style links to markdown syntax
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janosh committed Sep 13, 2023
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## v2023.5.31

- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" `#3022 <https://github.com/materialsproject/pymatgen/pull/3022>`_
- Unignore ruff PD011 `#3020 <https://github.com/materialsproject/pymatgen/pull/3020>`_
- Tweak variable names `#3019 <https://github.com/materialsproject/pymatgen/pull/3019>`_
- MaterialsProjectCompatibility issue silencable deprecation warning `#3017 <https://github.com/materialsproject/pymatgen/pull/3017>`_
- Optimize cython find_points_in _spheres `#3015 <https://github.com/materialsproject/pymatgen/pull/3015>`_
- Cp2k 2.0 `#2672 <https://github.com/materialsproject/pymatgen/pull/2672>`_
- Added methods to compute and compare DOS fingerprints `#2772 <https://github.com/materialsproject/pymatgen/pull/2772>`_
- Breaking: Overhaul class PymatgenTest `#3014 <https://github.com/materialsproject/pymatgen/pull/3014>`_
- Fix ValueError when structure.selective_dynamics has type np.array `#3012 <https://github.com/materialsproject/pymatgen/pull/3012>`_
- Clean up `#3010 <https://github.com/materialsproject/pymatgen/pull/3010>`_
- Update .pytest-split-durations `#3005 <https://github.com/materialsproject/pymatgen/pull/3005>`_
- Lookup MPRester API key in settings if None provided as arg `#3004 <https://github.com/materialsproject/pymatgen/pull/3004>`_
- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) `#3003 <https://github.com/materialsproject/pymatgen/pull/3003>`_
- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None `#3002 <https://github.com/materialsproject/pymatgen/pull/3002>`_
- Species parse oxi state from symbol str `#2998 <https://github.com/materialsproject/pymatgen/pull/2998>`_
- Re-export SiteCollection + DummySpecies from pymatgen.core `#2995 <https://github.com/materialsproject/pymatgen/pull/2995>`_
- Orbital-resolved icohplist `#2993 <https://github.com/materialsproject/pymatgen/pull/2993>`_
- Hide all type-hint-only imports behind if TYPE_CHECKING `#2992 <https://github.com/materialsproject/pymatgen/pull/2992>`_
- Add type hints for pymatgen.io.ase module `#2991 <https://github.com/materialsproject/pymatgen/pull/2991>`_
- Enable ruff doc rules in CI `#2990 <https://github.com/materialsproject/pymatgen/pull/2990>`_
- Suspected Typo Fix in pymatgen.io.vasp.optics `#2989 <https://github.com/materialsproject/pymatgen/pull/2989>`_
- Doc strings `#2987 <https://github.com/materialsproject/pymatgen/pull/2987>`_
- Fix average error `#2986 <https://github.com/materialsproject/pymatgen/pull/2986>`_
- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports `#2981 <https://github.com/materialsproject/pymatgen/pull/2981>`_
- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) `#3022 <https://github.com/materialsproject/pymatgen/pull/3022>`_
- fix unwanted x margins in get_elt_projected_plots_color (closes #562) `#562 <https://github.com/materialsproject/pymatgen/issues/562>`_
- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) `#2756 <https://github.com/materialsproject/pymatgen/issues/2756>`_
- add doc str explaining need for class ElementBase (closes #2999) `#2999 <https://github.com/materialsproject/pymatgen/issues/2999>`_
- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" [#3022](https://github.com/materialsproject/pymatgen/pull/3022)
- Unignore ruff PD011 [#3020](https://github.com/materialsproject/pymatgen/pull/3020)
- Tweak variable names [#3019](https://github.com/materialsproject/pymatgen/pull/3019)
- MaterialsProjectCompatibility issue silencable deprecation warning [#3017](https://github.com/materialsproject/pymatgen/pull/3017)
- Optimize cython find_points_in _spheres [#3015](https://github.com/materialsproject/pymatgen/pull/3015)
- Cp2k 2.0 [#2672](https://github.com/materialsproject/pymatgen/pull/2672)
- Added methods to compute and compare DOS fingerprints [#2772](https://github.com/materialsproject/pymatgen/pull/2772)
- Breaking: Overhaul class PymatgenTest [#3014](https://github.com/materialsproject/pymatgen/pull/3014)
- Fix ValueError when structure.selective_dynamics has type np.array [#3012](https://github.com/materialsproject/pymatgen/pull/3012)
- Clean up [#3010](https://github.com/materialsproject/pymatgen/pull/3010)
- Update .pytest-split-durations [#3005](https://github.com/materialsproject/pymatgen/pull/3005)
- Lookup MPRester API key in settings if None provided as arg [#3004](https://github.com/materialsproject/pymatgen/pull/3004)
- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) [#3003](https://github.com/materialsproject/pymatgen/pull/3003)
- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None [#3002](https://github.com/materialsproject/pymatgen/pull/3002)
- Species parse oxi state from symbol str [#2998](https://github.com/materialsproject/pymatgen/pull/2998)
- Re-export SiteCollection + DummySpecies from pymatgen.core [#2995](https://github.com/materialsproject/pymatgen/pull/2995)
- Orbital-resolved icohplist [#2993](https://github.com/materialsproject/pymatgen/pull/2993)
- Hide all type-hint-only imports behind if TYPE_CHECKING [#2992](https://github.com/materialsproject/pymatgen/pull/2992)
- Add type hints for pymatgen.io.ase module [#2991](https://github.com/materialsproject/pymatgen/pull/2991)
- Enable ruff doc rules in CI [#2990](https://github.com/materialsproject/pymatgen/pull/2990)
- Suspected Typo Fix in pymatgen.io.vasp.optics [#2989](https://github.com/materialsproject/pymatgen/pull/2989)
- Doc strings [#2987](https://github.com/materialsproject/pymatgen/pull/2987)
- Fix average error [#2986](https://github.com/materialsproject/pymatgen/pull/2986)
- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports [#2981](https://github.com/materialsproject/pymatgen/pull/2981)
- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) [#3022](https://github.com/materialsproject/pymatgen/pull/3022)
- fix unwanted x margins in get_elt_projected_plots_color (closes #562) [#562](https://github.com/materialsproject/pymatgen/issues/562)
- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) [#2756](https://github.com/materialsproject/pymatgen/issues/2756)
- add doc str explaining need for class ElementBase (closes #2999) [#2999](https://github.com/materialsproject/pymatgen/issues/2999)
- Update docs. `3e3c31c <https://github.com/materialsproject/pymatgen/commit/3e3c31c8d342c84f2c6bbb961c321e458b9accb9>`_
- ruff set isort.split-on-trailing-comma = false `c0ec534 <https://github.com/materialsproject/pymatgen/commit/c0ec53452c3dc87c6cca5edc1c6b2b6218f15569>`_

Expand All @@ -169,43 +169,43 @@ On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results

Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds.

For more details see `#2968 <https://github.com/materialsproject/pymatgen/pull/2968>`_and `#2969 <https://github.com/materialsproject/pymatgen/pull/2969>`_.
For more details see [#2968](https://github.com/materialsproject/pymatgen/pull/2968)and [#2969](https://github.com/materialsproject/pymatgen/pull/2969).

What's Changed

- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in `#2907 <https://github.com/materialsproject/pymatgen/pull/2907>`_
- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in `#2908 <https://github.com/materialsproject/pymatgen/pull/2908>`_
- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in `#2909 <https://github.com/materialsproject/pymatgen/pull/2909>`_
- Update team.rst by @jmmshn in `#2912 <https://github.com/materialsproject/pymatgen/pull/2912>`_
- Faff by @janosh in `#2915 <https://github.com/materialsproject/pymatgen/pull/2915>`_
- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in `#2916 <https://github.com/materialsproject/pymatgen/pull/2916>`_
- Modified dosplotter by @kaueltzen in `#2844 <https://github.com/materialsproject/pymatgen/pull/2844>`_
- auto version by @jmmshn in `#2925 <https://github.com/materialsproject/pymatgen/pull/2925>`_
- bug fix for potcar parsing by @jmmshn in `#2910 <https://github.com/materialsproject/pymatgen/pull/2910>`_
- Fix breaking changes from pandas v2 by @janosh in `#2935 <https://github.com/materialsproject/pymatgen/pull/2935>`_
- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in `#2927 <https://github.com/materialsproject/pymatgen/pull/2927>`_
- fix on reading multiple route in Gaussian input file by @Ameyanagi in `#2939 <https://github.com/materialsproject/pymatgen/pull/2939>`_
- Fix CI errors by @janosh in `#2940 <https://github.com/materialsproject/pymatgen/pull/2940>`_
- Add ResParser support for reading files with spin values by @ScottNotFound in `#2941 <https://github.com/materialsproject/pymatgen/pull/2941>`_
- Ignore bad unicode characters in Structure.from_file() by @janosh in `#2948 <https://github.com/materialsproject/pymatgen/pull/2948>`_
- Minor modification for symmetrically distinct Miller index generation by @fyalcin in `#2949 <https://github.com/materialsproject/pymatgen/pull/2949>`_
- Fixed Wulff shape for new versions of matplotlib by @CifLord in `#2950 <https://github.com/materialsproject/pymatgen/pull/2950>`_
- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in `#2953 <https://github.com/materialsproject/pymatgen/pull/2953>`_
- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in `#2954 <https://github.com/materialsproject/pymatgen/pull/2954>`_
- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in `#2945 <https://github.com/materialsproject/pymatgen/pull/2945>`_
- self.assertArrayEqual->assert by @janosh in `#2955 <https://github.com/materialsproject/pymatgen/pull/2955>`_
- fix GaussianOutput bug with multiple route lines by @xjf729 in `#2937 <https://github.com/materialsproject/pymatgen/pull/2937>`_
- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in `#2951 <https://github.com/materialsproject/pymatgen/pull/2951>`_
- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in `#2962 <https://github.com/materialsproject/pymatgen/pull/2962>`_
- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in `#2959 <https://github.com/materialsproject/pymatgen/pull/2959>`_
- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in `#2960 <https://github.com/materialsproject/pymatgen/pull/2960>`_
- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in `#2963 <https://github.com/materialsproject/pymatgen/pull/2963>`_
- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in `#2961 <https://github.com/materialsproject/pymatgen/pull/2961>`_
- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in `#2964 <https://github.com/materialsproject/pymatgen/pull/2964>`_
- Link /addons from new subsection on /contributing page by @janosh in `#2967 <https://github.com/materialsproject/pymatgen/pull/2967>`_
- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in `#2969 <https://github.com/materialsproject/pymatgen/pull/2969>`_
- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in `#2973 <https://github.com/materialsproject/pymatgen/pull/2973>`_
- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in `#2972
- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in [#2907](https://github.com/materialsproject/pymatgen/pull/2907)
- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in [#2908](https://github.com/materialsproject/pymatgen/pull/2908)
- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in [#2909](https://github.com/materialsproject/pymatgen/pull/2909)
- Update team.rst by @jmmshn in [#2912](https://github.com/materialsproject/pymatgen/pull/2912)
- Faff by @janosh in [#2915](https://github.com/materialsproject/pymatgen/pull/2915)
- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in [#2916](https://github.com/materialsproject/pymatgen/pull/2916)
- Modified dosplotter by @kaueltzen in [#2844](https://github.com/materialsproject/pymatgen/pull/2844)
- auto version by @jmmshn in [#2925](https://github.com/materialsproject/pymatgen/pull/2925)
- bug fix for potcar parsing by @jmmshn in [#2910](https://github.com/materialsproject/pymatgen/pull/2910)
- Fix breaking changes from pandas v2 by @janosh in [#2935](https://github.com/materialsproject/pymatgen/pull/2935)
- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in [#2927](https://github.com/materialsproject/pymatgen/pull/2927)
- fix on reading multiple route in Gaussian input file by @Ameyanagi in [#2939](https://github.com/materialsproject/pymatgen/pull/2939)
- Fix CI errors by @janosh in [#2940](https://github.com/materialsproject/pymatgen/pull/2940)
- Add ResParser support for reading files with spin values by @ScottNotFound in [#2941](https://github.com/materialsproject/pymatgen/pull/2941)
- Ignore bad unicode characters in Structure.from_file() by @janosh in [#2948](https://github.com/materialsproject/pymatgen/pull/2948)
- Minor modification for symmetrically distinct Miller index generation by @fyalcin in [#2949](https://github.com/materialsproject/pymatgen/pull/2949)
- Fixed Wulff shape for new versions of matplotlib by @CifLord in [#2950](https://github.com/materialsproject/pymatgen/pull/2950)
- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in [#2953](https://github.com/materialsproject/pymatgen/pull/2953)
- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in [#2954](https://github.com/materialsproject/pymatgen/pull/2954)
- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in [#2945](https://github.com/materialsproject/pymatgen/pull/2945)
- self.assertArrayEqual->assert by @janosh in [#2955](https://github.com/materialsproject/pymatgen/pull/2955)
- fix GaussianOutput bug with multiple route lines by @xjf729 in [#2937](https://github.com/materialsproject/pymatgen/pull/2937)
- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in [#2951](https://github.com/materialsproject/pymatgen/pull/2951)
- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in [#2962](https://github.com/materialsproject/pymatgen/pull/2962)
- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in [#2959](https://github.com/materialsproject/pymatgen/pull/2959)
- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in [#2960](https://github.com/materialsproject/pymatgen/pull/2960)
- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in [#2963](https://github.com/materialsproject/pymatgen/pull/2963)
- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in [#2961](https://github.com/materialsproject/pymatgen/pull/2961)
- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in [#2964](https://github.com/materialsproject/pymatgen/pull/2964)
- Link /addons from new subsection on /contributing page by @janosh in [#2967](https://github.com/materialsproject/pymatgen/pull/2967)
- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in [#2969](https://github.com/materialsproject/pymatgen/pull/2969)
- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in [#2973](https://github.com/materialsproject/pymatgen/pull/2973)
- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in [#2972](https://github.com/materialsproject/pymatgen/pull/2972)

## v2023.3.23

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